[Gnumed-devel] Incoming HL7 result microbiology report handling

[Jim Busser]

In the message below, 4th ORC OBR (Stool culture) we see a variety of OBX 
patterns. The cleanest end result would be 4 rows in test_result:

- a val_alpha comment

        Specimen #1\.br\
        - 10 day cold enrichment for Yersinia \.br\
        is performed on all stool specimens.\.br\
        Further report will follow if positive.\.br


        - Result phoned to physician's office \.br\

- a second val_alpha comment

- a third val_alpha row (Organism 1 result including *its* antibiotic 
sensitivity information)

- a fourth val_alpha row (Organism 2 result, including all *its* antibiotic 
sensitivity information)


Question:

If we stuff all the above Organism identification and culture and sensitivity 
results in a test_result table cell, how does the user properly "see" it? A 
tooltip comes to mind, *but* we already use measurement result tooltips to 
display metadata (see screen shot).

-- Jim (sig 1)

*********************************************************************
Administrivia:

just my notes on what the program logic should have to identify. The message 
contains…

- a few OBX segments which have a value type (field 3) of 'FT' which identify

        - technique for Yersinia included
        - result phoned
        - organism 1 E coli light growth
        - organism 2 Salmonella

- many more that are of value type 'ST' (short text)

The trick here is that the two OBX which are simply comments contain (to the 
right of their LOINC^Lab name for test) an empty field for

        OBX 005 Observation sub-ID

whereas the organisms (and the OBX pertaining to that organism) contain, in the 
case of organism 1, a data type of "short text" with value of '1' and -- in the 
case of organism 2 -- similar with sub-ID of '2'.

This means that when writing incoming message results, the relationship between 
OBX and rows to be created in clin.test_result should be

        where OBX 005 is empty ('||')
        --> create a row and put result in val_alpha

        where OBX 005 exhibits a change and is non-empty ('1')
        --> create a row and put result in val_alpha

        where OBX 005 exhibits no change and is non-empty (subsequent '1' s)
        --> append to val_alpha:
                (I would suggest an internal new line delimiter then ||) \
                OBX 003 Observation Identifier (LOINC^lab result name) || 
'space' || \
                OBX 005 'ST value' (here 'R / S' for Resistant / Sensitive)

-- Jim (sig 2)

******************************************

MSH|^~\&|SENDER_APP|MDS|HTTPCLIENT|vendor1|20050628140722||ORU^R01|MDC20050628140721957|P|2.3|||ER|AL
PID|||||DEMO^APATIENT||19770726|M|||260-4400 DOMI 
AVENUE\.br\COQUITLAM\.br\BC\.br\||(604)999-9999
ORC|RE||05-994065004-SC-1|||||||||90909^MDCARE^BOB
OBR|5||05-994065004-SC-1|SC^Stool 
Culture||20050506135300|20050506135300|||||||20050506135300||90909^MDCARE^BOB||||||20050512094510||MICRO|C|||90909^MDCARE^BOB
OBX|1|FT|X805^Comment||- Specimen #1\.br\- 10 day cold enrichment for Yersinia 
\.br\is performed on all stool specimens.\.br\Further report will follow if 
positive.\.br\||||||F|||20050512094510
OBX|2|FT|X10025^Comment||- Result phoned to physician's office 
\.br\||||||F|||20050512094510
OBX|3|FT|X433^Organism 1|1|ESCHERICHIA COLI\.Zt\LIGHT 
GROWTH\.br\||||||F|||20050512094510
OBX|4|ST|28-1^Ampicillin|1|S||||||F|||20050512094510
OBX|5|ST|X10042^Cephalothin/Cephalexin|1|R||||||C|||20050512094510
NTE|||Org1 Previously Reported As:  S
OBX|6|ST|476-2^Sulfonamide|1|S||||||F|||20050512094510
OBX|7|ST|516-5^Trimethoprim-Sulfa|1|S||||||F|||20050512094510
OBX|8|ST|185-9^Ciprofloxacin|1|S||||||F|||20050512094510
OBX|9|ST|367-3^Norfloxacin|1|S||||||F|||20050512094510
OBX|10|ST|267-5^Gentamicin|1|S||||||F|||20050512094510
OBX|11|ST|496-0^Tetracycline|1|S||||||F|||20050512094510
OBX|12|ST|173-5^Chloramphenicol|1|S||||||F|||20050512094510
OBX|13|ST|351-7^Nalidixic Acid|1|S||||||F|||20050512094510
OBX|14|ST|363-2^Nitrofurantoin|1|S||||||F|||20050512094510
OBX|15|FT|X10019^Organism 2|2|SALMONELLA SPECIES\.Zt\MODERATE 
GROWTH\.br\||||||F|||20050512094510
OBX|16|ST|28-1^Ampicillin|2|S||||||F|||20050512094510
OBX|17|ST|X10042^Cephalothin/Cephalexin|2|S||||||F|||20050512094510
OBX|18|ST|233-7^Erythromycin|2|S||||||F|||20050512094510
OBX|19|ST|516-5^Trimethoprim-Sulfa|2|S||||||F|||20050512094510
OBX|20|ST|185-9^Ciprofloxacin|2|S||||||F|||20050512094510
OBX|21|ST|367-3^Norfloxacin|2|S||||||F|||20050512094510
OBX|22|ST|267-5^Gentamicin|2|S||||||F|||20050512094510
OBX|23|ST|496-0^Tetracycline|2|S||||||F|||20050512094510
OBX|24|ST|173-5^Chloramphenicol|2|S||||||F|||20050512094510
OBX|25|ST|351-7^Nalidixic Acid|2|S||||||F|||20050512094510
OBX|26|ST|363-2^Nitrofurantoin|2|S||||||F|||20050512094510
OBX|27|ST|X084^Polymixin B|2|S||||||F|||20050512094510

-- Jim (sig 3)